I am writing to get input from experienced ones. I got nanopore data and using q2ONT command line to process my 16srRNA gene seq data. After demuliplexing, adapters removal, and trimming the reads to 1400 length, i imported my sequencing data into qiime2.
I used these commands for deprelication of sequences, and for obtaining feature table seqs and feature table summary.
Dereplication of sequences
qiime vsearch dereplicate-sequences
qiime feature-table tabulate-seqs
qiime feature-table summarize
After these steps, i got two files, derep-seqs.qzv and derep-table.qzv.
Upon checking derep-table.qzv using qiime2 view, i realized that something might have gone wrong, as Frequency per feature is showing 1. Photo is attached.
I later run the command vsearch command using --verbose and below is the outcome of the command.
vsearch v2.7.0_linux_x86_64, 15.3GB RAM, 16 cores
Reading file /tmp/q2-QIIME1DemuxDirFmt-hvrikd0d/seqs.fna 100%
90956600 nt in 64969 seqs, min 1400, max 1400, avg 1400
64969 unique sequences, avg cluster 1.0, median 1, max 1
Writing output file 100%
Writing uc file, first part 100%
Writing uc file, second part 100%
Although i have many unique features but they are counted as 1. The question is why unique features are equal to number of reads in my samples? Does it mean dereplication is considering each read as unique feature? If so, what should be the solution to resolve this problem?
Could you please provide insights what could have gone wrong that i obtained such outcomes, or it is normal to get such outcomes while processing nanopore seq data?